Clinical applications of human pluripotent stem cells (PSCs) are limited by the lack of chemically well-defined scaffolds for cell expansion, differentiation and implantation. In this study, we systematically screened various self-assembling hexapeptides to identify the best matrix for long-term 3D PSC culture. Lysine-containing Ac-ILVAGK-NH2 hydrogels maintained best the pluripotency of human embryonic and induced PSCs even after 30 passages. This peptide matrix is also compatible with the use of xeno-free and defined differentiation media. By exploiting its stimuli-responsive sol-gel transition, arrays of encapsulated PSCs can be bioprinted for large-scale cell expansion and derivation of miniaturized organoid cultures for high-throughput screening.